I actually don't like fandoms in general so I'm not familiar with many. I can't put my finger specifically on the reason, but any I've been exposed to seem to have a lot of in-fighting and are really sensitive, temperamental, unwilling to let go, or never staisfied. I guess they just seem really high-strung to me.
I really loved the Avatar: the Last Airbender/Legend of Korra fandom up until the finale but they reacted so badly turning on each other like they did. Now that things have somewhat settled they're okay again.
I also hate the big three fangirl - Sherlock, Supernatural, and Doctor Who, the last one particularly because I grew up watching the old series and they've just made me never feel like catching up in the new series.
Fangirls ruin a lot I guess because they seem to be the ones who ship everything that moves and that gets old.

Like I said, I do like Naruto (really like the manga more than anime). I do agree with you on first part of the series & got the chance to read Kakashi Gaiden arc/saga (truly great). As for Naruto Shippuden (second part of series), it was tab bit more miss than hits. The series dragged on for way too long, flashback fiesta (I don't mind some of them. But, way too much of that can ruin it for everybody else) & political nonsense (as you stated). As for the ending, I've mixed opinions on that. I don't detest the series at all. There are some things I just don't like, fanbase are just buckwild & nutty. One question, what do you mean "the series became too convoluted"?

Ugh, I shouldn't have used the word "convoluted" even though, in one sense, I did mean that. For me, the politics grew too complex, redundant and overbearing - I felt that Naruto lost much of the essence of its main themes, its wonderful charm and truly great story arcs - all of which the first half was full of, and what made it so memorable.

What I really want to compare the second half of Naruto to....Is an onion. Yes I know; bear with me. Onions have multiple layers to peel before finally reaching the long awaited center. That is exactly what the second half of Naruto was like. Peeling layer after layer after layer - only to find yet another, far more complex layer underneath. The plot became ridiculous, the villains even more so. Characterization was especially murdered by the finale and at that point we all knew the series should have ended long (long) ago.

Personally....I still feel that Orochimaru and the Akatsuki should have been the main and only villains of the story. Adding villain after villain, one more powerful than the next became utterly ridiculous and made the characterization really be spread thin across so many characters and so many continuously popping up) intricacies. I feel that the story lost aim of itself after introducing way too many characters and inter-connecting story lines. It was just too much, too much. Kishi had a great basis, a great world - he just went overboard with it and really took apart his story all by himself. What a pity.

In terms of characters...

Sakura should have continuously grown and matured, and not ended with a murderous sociopath; I felt that was such a degradation of her character, or what her character could have become under a more capable author. Letting her end up with such an abusive, psychopathic man all on the basis of a painfully shallow crush of a 12 year old girl that never truly developed just reverts her characterization back to the horrible child she was in the first half.

I will always feel that Sasuke should have died at the end, gone down with his Clan instead of being allowed to life scotch free after all the shit he caused. Hinata should have either only loved Naruto in a platonic way and admired him as an inspiration, or she should have grown up and over her crush on him. She should have also grown into her Clan head - wtf happened to that plot line? Sakura and Naruto - who had the most development, most screen time, devotion and characterization together should have ended up together; it would have been great for Sakura's character, and we would have gotten to see the result of Naruto's feelings for her as they grew from being a shallow crush to that true bond they shared. Neji should have absolutely never died but live to see the Hyuuga rejoined and taken a main place in the Clan beside Hinata. Naruto of course should have become Hokage with Sakura as the chief medical ninja - the series should have ended with Naruto looking over the same old un-modernized Konoha and the family he has finally found for himself. No kids shown or excessive coupling - just that ending or something similar.

Wow. You broke it down so easily & straight to the point. Akatsuki & Orochimaru have no business being pushed to the side for more villain (couple of them are powerful) in Naruto Shippuden. I didn't see Neji being killed off coming at all. I get what you're saying on Hinata & it sounds like give her everything type of thing. Two things that bug me about Naruto are he couldn't become Hokage without saving Sasuke & blindly chasing after Sakura (I'll get to her). I'm just glad they're friends at the end (not an couple). Also, I'm happy that Naruto's the seventh Hokage. Who's the chief medical ninja anyway? As for Sasuke, I wouldn't kill him off at all. Instead, I'd lock him up for life for unspeakable crimes. Speaking of Sakura, what a trainwreck of her. She goes from having an stupid crush on Sasuke to being married with an daughter. Everything's all good in the village, lol!

I've never had any problems with My Little Pony fans, despite them having a rather notorious reputation. I don't normally interact with people I don't know over the internet, whether it be comment sections, message boards, etc., but whenever I see a brony make any sort of comment, be it witty, stupid, or whatever, there is always at least one person who disregards everything they say because they're a 'bronyfag'. It makes me kind of sad, because they're normally good people who just happen to like something other people despise.

That being said, I think there is a pretty big problem with the idea of fandoms. There are a group of people who all enjoy one thing. Some of these people like said thing a little too much, and start becoming rabidly defensive about this thing. The 'normal' fans see this and don't want to associate with these kinds of people, drifting away from the group of people. This leaves behind mostly those who are obsessive over their point of interest, and due to the vocal nature of such people, the fandom will get a bad reputation among other internet communities,

Best: Whovians. They are so wonderfully weird, random, and awkward, all of them. Or, at least the ones I've met. I tried to get into it but I was too lazy to catch up and I was too into books and anime, soo....
Worst: Bronies. More specifically, the more vocal ones. Those ones tend to be super obnoxious. I know quite a few Bronies and most of them aren't too obnoxious about MLP, (they're more obnoxious about Hetalia) but everywhere else I see a Brony, I usually really wish they would shut up.

Not the easiest question for me to answer, since I have been in fandom for a very long time, but I get a little jealous of big fandoms (e.g. TV shows like Supernatural, the Marvel movies) that hoover up fans from anime / manga and video game fandom. Especially the JRPG branch of video game fandom. Our numbers have been about the same since the late '90s, and most of us know each other. (And yes, we are still exasperated that Final Fantasy VII has so many fans despite being a game – never remade – that is older than most of fandom.) A little new blood would be nice.

I haven't been exposed to very many fandoms seeing as i dont go to cons or other social gatherings where people meet to talk about they're love for "vyx subject". however here's my worst and best expirence with the two i have been exposed to.

Worst: dc/marvel fans, i was in a comic book store once getting my monthly fix. had a conversation with a guy in there and he punched me for saying i dont like superman because he comes off as too "boy scout-ish".

Best: walking dead seems to have a nice group of people... dont really seem to argue things one way or the other they just eventually come to agree that "yeah they could write that in".

I'm really interested in a lot of things like Star Wars and stuff and in my opinion people can like/obsess over what they like as long as they actually listen to other people's interest and respect it. Although I'm a big fan of Star Wars, I listen to people that may not like it and I respect their opinions on why they don't like it. So the point is, I think best fandom could vary. As long as they are willing to accept some people might not like their interest as much as they do and respect other fandoms, I'm good with that.